R/plot.davesil.R

In dave: Functions for "Data Analysis in Vegetation Ecology"

# plot method for davesil()
#
# This delivers a silhouette plot from an object o.sil of
# class "silhouette". Unlike the original plot it requires
# o.hclust from where it takes the case
# labels plotted in front of the bars. Groups are distinguished by gray levels or colors.
# To plot Figure 5.5 use par(mfrow=c(3,1),omi=c(0,0,0,0),mar=c(3,1,1,1))
# NOTE: axes and legends suppressing to plot Figure 5.8

plot.davesil<- function(x,...,range=NULL) {
    o.davesil<- x
    test<- is.null(range)
    ndim<- length(o.davesil$o.relgr)
    if(test == TRUE) range<- c(1,ndim)
    n<- range[2]-range[1]+1
    # organize o.sil like output of function silhouette
    o.sil<- cbind(o.davesil$o.relgr,o.davesil$second,o.davesil$swidth)
    #
    oo.sil<- o.sil[order(o.sil[,3]),]
    ooo.sil<-oo.sil[order(oo.sil[,1]),]
    ooo.sil<- ooo.sil[range[1]:range[2],]
    groups<- unique(ooo.sil[,1])
    ng<- length(groups)
    ngroups<- length(groups)-1
    tgroups<- table(ooo.sil[,1])
    space<- rep(0,n)
    yc<- seq(1,n,1)
    pos<- 0
    if(ngroups > 0) {
        for (i in 1:ngroups) {
            pos<- pos+tgroups[i]
            space[pos+1]<- 0.2
        }
    }
    for (i in 1:n) yc[i]<- yc[i]+sum(space[1:i])
    #  cat("ngroups ",ngroups,"\n")
    #  cat("groups ",groups,"\n")
    #  cat("tgroups ",tgroups,"\n")
    #  cat("space ",space,"\n")
    #  cat("yc ",yc,"\n")
    #
    # Evaluating the use of colours
    r<- rainbow(ng)
    colbar<- gray(0.9/ooo.sil[,1]^0.5)
    colbar<- r[ooo.sil[,1]]                       # turn color off here
    colleg<- gray(0.9/(unique(ooo.sil[,1]))^0.5)
    colleg<- r
    #
    n1<- o.davesil$names
    n2<- n1[order(o.sil[,3])]
    n3<- n2[order(oo.sil[,1])]
    n3<- n3[range[1]:range[2]]
    par(tcl=-0.3,mgp=c(2,0.5,0))
    barplot(ooo.sil[,3],space=space,horiz=TRUE,border=0,xlim=c(-0.4,1),xlab="Silhouette width",yaxt="n",col=colbar, cex.axis=0.8,cex.lab=0.8,xpd=TRUE,srt=0,axisnames=FALSE,axes=TRUE)
    legend("topright",table(ooo.sil[,1]),paste("group no.",unique(ooo.sil[,1])),pch=15,col=colleg,bty="n",cex=0.8)
    # These are the releve numbers on the left hand side of the barplot. Fontsize is a heuristic function of ndim:
    textsize<- 3.5/ndim^0.5
    # cat("textsize ",textsize,"\n")
    text(rep(-0.35,ndim),yc,n3,cex=textsize,pos=1,offset=0.0,adj=c(1,0))
}